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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
InCroMAP Resource Report Resource Website 10+ mentions |
InCroMAP (RRID:SCR_012964) | InCroMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5,2023. Integrated analysis of cross-platform microarray and pathway data. | is listed by: OMICtools | PMID:23257199 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00855 | SCR_012964 | 2026-08-29 11:24:25 | 11 | ||||||||
|
TraceTuner Resource Report Resource Website 10+ mentions |
TraceTuner (RRID:SCR_013019) | TraceTuner | software resource | Software tool for base and quality calling of trace files from DNA sequencing instruments. |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
Free | OMICS_01158 | https://sources.debian.org/src/tracetuner/ | SCR_013019 | TraceTuner - DNA sequencing quality values base calling and trace processing | 2026-08-29 11:24:36 | 14 | |||||||
|
GenomeView Resource Report Resource Website 10+ mentions |
GenomeView (RRID:SCR_012968) | GenomeView | data or information resource, database, software resource | A next-generation stand-alone genome browser and editor initiated in the BSB group at VIB and currently developed at Broad Institute. | is listed by: OMICtools | PMID:22102585 | OMICS_00913 | SCR_012968 | 2026-08-29 11:24:25 | 36 | |||||||||
|
seqMINER Resource Report Resource Website 100+ mentions |
seqMINER (RRID:SCR_013020) | seqMINER | software resource | Software for a genome wide mapping data interpretation platform for NGS (ChIPSeq). | java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21177645 | GNU General Public License, v3 | biotools:seqminer, OMICS_00460 | https://bio.tools/seqminer | SCR_013020 | 2026-08-29 11:24:26 | 190 | ||||||
|
MIREAP Resource Report Resource Website 100+ mentions |
MIREAP (RRID:SCR_013025) | MIREAP | software resource | A software tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00376 | SCR_013025 | 2026-08-29 11:24:26 | 389 | |||||||||
|
MIReNA Resource Report Resource Website 1+ mentions |
MIReNA (RRID:SCR_013024) | MIReNA | software resource | A software tool to find microRNAs with high accuracy and no learning at genome scale and from deep sequencing data. | is listed by: OMICtools | PMID:20591903 | Acknowledgement requested, CeCILL license | OMICS_00377 | SCR_013024 | 2026-08-29 11:24:36 | 8 | ||||||||
|
MIG Resource Report Resource Website 1+ mentions |
MIG (RRID:SCR_012972) | MIG | software resource | Allows the user to conveniently compare data from many loci., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00942 | SCR_012972 | Multi-Image Genome | 2026-08-29 11:24:26 | 1 | ||||||||
|
EDNA Resource Report Resource Website 10+ mentions |
EDNA (RRID:SCR_012981) | EDNA | software resource | Software for Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23990411 | Creative Commons Attribution NonCommercial License, v2 | OMICS_00974 | SCR_012981 | EDNA - Energy Based Multiple Sequence Alignment (MSA) for Binding Sites | 2026-08-29 11:24:25 | 34 | ||||||
|
cn.mops Resource Report Resource Website 10+ mentions |
cn.mops (RRID:SCR_013036) | cn.mops | software resource | A data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
biotools:cn.mops, OMICS_00335 | https://bio.tools/cn.mops | SCR_013036 | Copy Number estimation by a Mixture Of PoissonS | 2026-08-29 11:24:36 | 10 | |||||||
|
SAMZIP Resource Report Resource Website |
SAMZIP (RRID:SCR_012980) | SAMZIP | software resource | An encoding and decoding tool for Sequence Alignment/Map (SAM) files. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22164252 | OMICS_00967 | SCR_012980 | 2026-08-29 11:24:35 | 0 | |||||||||
|
TopHat Resource Report Resource Website 5000+ mentions Rating or validation data |
TopHat (RRID:SCR_013035) | alignment software, data analysis software, data processing software, image analysis software, sequence analysis software, software application, software resource | Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions. | align, RNA-Seq, read, cDNA, sequencing, transcriptomics, fast, splice, junction, mapper, exon, analysis, bio.tools |
uses: Bowtie is used by: CIRCexplorer is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: HISAT2 has parent organization: University of Maryland; Maryland; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Johns Hopkins University; Maryland; USA has parent organization: University of Washington; Seattle; USA works with: GeneScissors |
NHGRI R01 HG006102; NHGRI R01 HG006677 |
PMID:23618408 PMID:19289445 DOI:10.1093/bioinformatics/btp120 |
Free, Available for download, Freely available | biotools:tophat, OMICS_01257 | https://github.com/infphilo/tophat, https://bio.tools/tophat, https://sources.debian.org/src/tophat/ | http://tophat.cbcb.umd.edu/ | SCR_013035 | tophat, TopHat1, Tophat2 | 2026-08-29 11:24:28 | 9789 | ||||
|
SAMMate Resource Report Resource Website 10+ mentions |
SAMMate (RRID:SCR_013037) | SAMMate | software resource | An open source GUI software suite to process RNA-Seq data. It is composed of two modules: assemblySAM and SAMMate. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
biotools:sammate, OMICS_01264 | https://bio.tools/sammate | SCR_013037 | 2026-08-29 11:24:26 | 11 | ||||||||
|
SHREC Resource Report Resource Website 10+ mentions |
SHREC (RRID:SCR_013009) | SHREC | software resource | A bioinformatics tool for error correction of HTS read data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01110 | SCR_013009 | 2026-08-29 11:24:26 | 14 | ||||||||||
|
hiCtools Resource Report Resource Website |
hiCtools (RRID:SCR_013010) | hiCtools | software resource | This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00522 | SCR_013010 | 2026-08-29 11:24:27 | 0 | |||||||||
|
LOCAS Resource Report Resource Website 1+ mentions |
LOCAS (RRID:SCR_013064) | LOCAS | software resource | A software to assemble short reads of next generation sequencing technologies at low coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21858125 | OMICS_00019, biotools:locas | https://bio.tools/locas | SCR_013064 | 2026-08-29 11:24:29 | 2 | |||||||
|
VDJFasta Resource Report Resource Website 1+ mentions |
VDJFasta (RRID:SCR_013069) | VDJFasta | software resource | Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19875695 | OMICS_00004 | SCR_013069 | 2026-08-29 11:24:27 | 9 | |||||||||
|
VCAKE Resource Report Resource Website 1+ mentions |
VCAKE (RRID:SCR_013060) | VCAKE | software resource | A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00037 | SCR_013060 | 2026-08-29 11:24:36 | 4 | ||||||||||
|
PRICE Resource Report Resource Website 100+ mentions |
PRICE (RRID:SCR_013063) | PRICE | software resource | Software for a de novo genome assembler implemented in C++. | c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Francisco; California; USA |
OMICS_01430, biotools:price | https://bio.tools/price | SCR_013063 | Paired-Read Iterative Contig Extension | 2026-08-29 11:24:27 | 165 | |||||||
|
HiTC Resource Report Resource Website 50+ mentions |
HiTC (RRID:SCR_013175) | HiTC | software resource | Software package to explore high-throughput ''C'' data such as 5C or Hi-C. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00524 | SCR_013175 | 2026-08-29 11:24:28 | 87 | ||||||||||
|
CoNIFER Resource Report Resource Website 100+ mentions |
CoNIFER (RRID:SCR_013213) | CoNIFER | software resource | Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. |
is listed by: OMICtools has parent organization: SourceForge |
Commercial license | OMICS_00330 | SCR_013213 | Copy Number Inference From Exome Reads | 2026-08-29 11:24:31 | 200 |
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